Include and wrap Glasgow Subgraph Solver (#221)

Add subgraph package to find subgraph isomorphisms (a.k.a. native embeddings)
  * added portable-snippets submodule
  * added glasgow subgraph solver submodule (temporarily using @boothby's fork)
  * added fake boost library
  * added note about submodules in python installation instructions

.circleci/config.yml

@@ -147,6 +147,11 @@ jobs:
 
     steps:
       - checkout
+      - run: &initialize-submodules
+          name: get submodules
+          command: |
+            git submodule init
+            git submodule update
       - setup_remote_docker
       - run-cibuildwheel
 
@@ -167,6 +172,7 @@ jobs:
 
     steps:
       - checkout
+      - run: *initialize-submodules
       - run-cibuildwheel
 
   build-and-test-osx:
@@ -186,6 +192,7 @@ jobs:
 
     steps:
       - checkout
+      - run: *initialize-submodules
       - run-cibuildwheel
 
   build-and-test-windows:
@@ -203,6 +210,7 @@ jobs:
 
     steps:
       - checkout
+      - run: *initialize-submodules
       - run-cibuildwheel
 
   deploy-all:
@@ -230,6 +238,7 @@ jobs:
 
     steps:
       - checkout
+      - run: *initialize-submodules
       - run:
           name: build sdist
           command: |
@@ -247,6 +256,7 @@ jobs:
 
     steps:
       - checkout
+      - run: *initialize-submodules
       - attach_workspace:
           at: dist
       - run:

.gitmodules

@@ -0,0 +1,6 @@
+[submodule "external/portable-snippets"]
+	path = external/portable-snippets
+	url = [email protected]:nemequ/portable-snippets.git
+[submodule "external/glasgow-subgraph-solver"]
+	path = external/glasgow-subgraph-solver
+	url = [email protected]:boothby/glasgow-subgraph-solver.git

MANIFEST.in

@@ -1,2 +1,4 @@
 global-include *.hpp
-include rectangle-packer/*/*
+recursive-include external/glasgow-subgraph-solver *.hh LICENSE
+recursive-include external/portable-snippets builtin.h COPYING.md
+recursive-include external/boost BOOST_LICENSE

README.rst

@@ -50,10 +50,16 @@ pypi. Source distributions are provided as well.
 
     pip install minorminer
 
-To install from this repository, run the `setuptools` script.
+To install from this repository, you will need to first fetch the submodules
+
+    git submodule init
+    git submodule update
+
+and then run the `setuptools` script.
 
 .. code-block:: bash
 
+
     pip install -r requirements.txt
     python setup.py install
     # optionally, run the tests to check your build

external/boost/BOOST_LICENSE

@@ -0,0 +1,23 @@
+Boost Software License - Version 1.0 - August 17th, 2003
+
+Permission is hereby granted, free of charge, to any person or organization
+obtaining a copy of the software and accompanying documentation covered by
+this license (the "Software") to use, reproduce, display, distribute,
+execute, and transmit the Software, and to prepare derivative works of the
+Software, and to permit third-parties to whom the Software is furnished to
+do so, all subject to the following:
+
+The copyright notices in the Software and this entire statement, including
+the above license grant, this restriction and the following disclaimer,
+must be included in all copies of the Software, in whole or in part, and
+all derivative works of the Software, unless such copies or derivative
+works are solely in the form of machine-executable object code generated by
+a source language processor.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE, TITLE AND NON-INFRINGEMENT. IN NO EVENT
+SHALL THE COPYRIGHT HOLDERS OR ANYONE DISTRIBUTING THE SOFTWARE BE LIABLE
+FOR ANY DAMAGES OR OTHER LIABILITY, WHETHER IN CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+DEALINGS IN THE SOFTWARE.

external/boost/bimap.hpp

@@ -0,0 +1,44 @@
+// Copyright 2022-2023 D-Wave Systems Inc.
+//
+//    Licensed under the Apache License, Version 2.0 (the "License");
+//    you may not use this file except in compliance with the License.
+//    You may obtain a copy of the License at
+//
+//        http://www.apache.org/licenses/LICENSE-2.0
+//
+//    Unless required by applicable law or agreed to in writing, software
+//    distributed under the License is distributed on an "AS IS" BASIS,
+//    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+//    See the License for the specific language governing permissions and
+//    limitations under the License.
+//
+// Excerpted from and/or inspired by implementations found in the Boost Library
+// see external/boost/BOOST_LICENSE or https://www.boost.org/LICENSE_1_0.txt
+
+#pragma once
+
+#include <boost/bimap/unordered_set_of.hpp>
+#include <unordered_map>
+#include <tuple>
+
+namespace boost {
+
+template<typename L, typename R, typename Alloc>
+class bimap;
+
+template<typename L, typename R, typename Alloc>
+class bimap<boost::bimaps::unordered_set_of<L>, boost::bimaps::unordered_set_of<R>, Alloc> {
+  public:
+    std::unordered_map<L, R> left;
+    std::unordered_map<R, L> right;
+    typedef typename std::pair<L, R> value_type;
+
+    void insert(const value_type v) {
+        left.insert(std::make_pair(v.first, v.second));
+        right.insert(std::make_pair(v.second, v.first));
+    }
+
+    bimap() {}
+};
+
+}

external/boost/bimap/unordered_set_of.hpp

@@ -0,0 +1,27 @@
+// Copyright 2022-2023 D-Wave Systems Inc.
+//
+//    Licensed under the Apache License, Version 2.0 (the "License");
+//    you may not use this file except in compliance with the License.
+//    You may obtain a copy of the License at
+//
+//        http://www.apache.org/licenses/LICENSE-2.0
+//
+//    Unless required by applicable law or agreed to in writing, software
+//    distributed under the License is distributed on an "AS IS" BASIS,
+//    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+//    See the License for the specific language governing permissions and
+//    limitations under the License.
+//
+// Excerpted from and/or inspired by implementations found in the Boost Library
+// see external/boost/BOOST_LICENSE or https://www.boost.org/LICENSE_1_0.txt
+
+#pragma once
+
+namespace boost::bimaps {
+
+template<typename T>
+class unordered_set_of {
+    typedef T value_type;
+};
+
+}

external/boost/container/allocator.hpp

@@ -0,0 +1,25 @@
+// Copyright 2022-2023 D-Wave Systems Inc.
+//
+//    Licensed under the Apache License, Version 2.0 (the "License");
+//    you may not use this file except in compliance with the License.
+//    You may obtain a copy of the License at
+//
+//        http://www.apache.org/licenses/LICENSE-2.0
+//
+//    Unless required by applicable law or agreed to in writing, software
+//    distributed under the License is distributed on an "AS IS" BASIS,
+//    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+//    See the License for the specific language governing permissions and
+//    limitations under the License.
+//
+// Excerpted from and/or inspired by implementations found in the Boost Library
+// see external/boost/BOOST_LICENSE or https://www.boost.org/LICENSE_1_0.txt
+
+#pragma once
+
+namespace boost::container {
+
+template<typename T> class allocator {};
+
+}
+

external/boost/functional/hash.hpp

@@ -0,0 +1,33 @@
+// Copyright 2022-2023 D-Wave Systems Inc.
+//
+//    Licensed under the Apache License, Version 2.0 (the "License");
+//    you may not use this file except in compliance with the License.
+//    You may obtain a copy of the License at
+//
+//        http://www.apache.org/licenses/LICENSE-2.0
+//
+//    Unless required by applicable law or agreed to in writing, software
+//    distributed under the License is distributed on an "AS IS" BASIS,
+//    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+//    See the License for the specific language governing permissions and
+//    limitations under the License.
+//
+// Excerpted from and/or inspired by implementations found in the Boost Library
+// see external/boost/BOOST_LICENSE or https://www.boost.org/LICENSE_1_0.txt
+
+#pragma once
+
+namespace boost {
+
+template <typename T>
+inline void hash_combine(std::size_t & seed, const T value) {
+  std::hash<T> h;
+  hash_combine(seed, h(value));
+}
+
+template <>
+inline void hash_combine(std::size_t & seed, const std::size_t value) {
+  seed ^= value + 0x9e3779b9 + (seed << 6) + (seed >> 2);
+}
+
+}

external/boost/iostreams/device/file.hpp

@@ -0,0 +1,32 @@
+// Copyright 2022-2023 D-Wave Systems Inc.
+//
+//    Licensed under the Apache License, Version 2.0 (the "License");
+//    you may not use this file except in compliance with the License.
+//    You may obtain a copy of the License at
+//
+//        http://www.apache.org/licenses/LICENSE-2.0
+//
+//    Unless required by applicable law or agreed to in writing, software
+//    distributed under the License is distributed on an "AS IS" BASIS,
+//    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+//    See the License for the specific language governing permissions and
+//    limitations under the License.
+//
+// Excerpted from and/or inspired by implementations found in the Boost Library
+// see external/boost/BOOST_LICENSE or https://www.boost.org/LICENSE_1_0.txt
+
+#pragma once
+
+#include <fstream>
+#include <iostream>
+#include <string>
+
+namespace boost::iostreams {
+
+std::ofstream file_sink(const std::string &fn) {
+    std::ofstream outfile;
+    outfile.open(fn);
+    return outfile;
+}
+
+}

external/boost/iostreams/filter/bzip2.hpp

@@ -0,0 +1,29 @@
+// Copyright 2022-2023 D-Wave Systems Inc.
+//
+//    Licensed under the Apache License, Version 2.0 (the "License");
+//    you may not use this file except in compliance with the License.
+//    You may obtain a copy of the License at
+//
+//        http://www.apache.org/licenses/LICENSE-2.0
+//
+//    Unless required by applicable law or agreed to in writing, software
+//    distributed under the License is distributed on an "AS IS" BASIS,
+//    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+//    See the License for the specific language governing permissions and
+//    limitations under the License.
+//
+// Excerpted from and/or inspired by implementations found in the Boost Library
+// see external/boost/BOOST_LICENSE or https://www.boost.org/LICENSE_1_0.txt
+
+#pragma once
+
+#include <stdexcept>
+
+namespace boost::iostreams {
+
+bool bzip2_compressor() {
+    throw std::runtime_error("filtering_ostream is not implemented");
+    return false;
+}
+
+}

external/boost/iostreams/filtering_stream.hpp

@@ -0,0 +1,36 @@
+// Copyright 2022-2023 D-Wave Systems Inc.
+//
+//    Licensed under the Apache License, Version 2.0 (the "License");
+//    you may not use this file except in compliance with the License.
+//    You may obtain a copy of the License at
+//
+//        http://www.apache.org/licenses/LICENSE-2.0
+//
+//    Unless required by applicable law or agreed to in writing, software
+//    distributed under the License is distributed on an "AS IS" BASIS,
+//    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+//    See the License for the specific language governing permissions and
+//    limitations under the License.
+//
+// Excerpted from and/or inspired by implementations found in the Boost Library
+// see external/boost/BOOST_LICENSE or https://www.boost.org/LICENSE_1_0.txt
+
+#pragma once
+
+#include <iostream>
+#include <streambuf>
+namespace boost::iostreams {
+
+class filtering_ostream: public std::basic_ostream<char> {
+    class fake_streambuf: public std::basic_streambuf<char> {
+      public:
+        fake_streambuf() : std::basic_streambuf<char>() {}
+    };
+    fake_streambuf sb;
+  public:
+    filtering_ostream() : sb(), basic_ostream(&sb) {}
+    template<typename T>
+    void push(T) { throw std::runtime_error("filtering_ostream is not implemented"); }
+};
+
+}

external/boost/iostreams/stream.hpp

@@ -0,0 +1,18 @@
+// Copyright 2022-2023 D-Wave Systems Inc.
+//
+//    Licensed under the Apache License, Version 2.0 (the "License");
+//    you may not use this file except in compliance with the License.
+//    You may obtain a copy of the License at
+//
+//        http://www.apache.org/licenses/LICENSE-2.0
+//
+//    Unless required by applicable law or agreed to in writing, software
+//    distributed under the License is distributed on an "AS IS" BASIS,
+//    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+//    See the License for the specific language governing permissions and
+//    limitations under the License.
+//
+// Excerpted from and/or inspired by implementations found in the Boost Library
+// see external/boost/BOOST_LICENSE or https://www.boost.org/LICENSE_1_0.txt
+
+#pragma once

external/boost/multiprecision/cpp_int.hpp

@@ -0,0 +1,24 @@
+// Copyright 2022-2023 D-Wave Systems Inc.
+//
+//    Licensed under the Apache License, Version 2.0 (the "License");
+//    you may not use this file except in compliance with the License.
+//    You may obtain a copy of the License at
+//
+//        http://www.apache.org/licenses/LICENSE-2.0
+//
+//    Unless required by applicable law or agreed to in writing, software
+//    distributed under the License is distributed on an "AS IS" BASIS,
+//    WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+//    See the License for the specific language governing permissions and
+//    limitations under the License.
+//
+// Excerpted from and/or inspired by implementations found in the Boost Library
+// see external/boost/BOOST_LICENSE or https://www.boost.org/LICENSE_1_0.txt
+
+#pragma once
+
+namespace boost::multiprecision {
+
+typedef long long int cpp_int;
+
+}